Pseudomonas syringae is a common foliar plant pathogenic bacterium that causes diseases on many crop plants. We hypothesized that today's highly virulent P. syringae crop pathogens with narrow host range might have evolved after the advent of agriculture from ancestral P. syringae strains with wide host range that were adapted to mixed plant communities. The model tomato and Arabidopsis pathogen P. syringae pv. tomato (Pto) DC3000 and its close relatives isolated from crop plants were thus selected to unravel basic principles of host range evolution by applying molecular evolutionary analysis and comparative genomics approaches. Phylogenetic analysis was combined with host range tests to reconstruct the host range of the most recent common ancestor of all analyzed strains isolated from crop plants. Even though reconstruction of host range of the most recent common ancestor of all analyzed strains was not conclusive, support for this hypothesis was found in some sub-groups of strains. The focus of my studies then turned to Pto T1, which was found to represent the most common P. syringae lineage causing bacterial speck disease on tomato world-wide. Five genomes were sequenced and compared to each other. Identical genotypes were found in North America and Europe suggesting frequent pathogen movement between these continents. Moreover, the type III-secreted effector gene hopM1 was found to be under strong selection for loss of function and non-synonymous mutations in the fliC gene allowed to identify a region that triggers plant immunity. Finally, Pto T1 was compared to closely related bacteria isolated from snow pack and surface water in the French Alps. Recombination between alpine strains and crop strains was inferred and virulence gene repertoires of alpine strains and crop strains were found to overlap. Alpine strains cause disease on tomato and have relatively wider host ranges than Pto T1. The conclusion from these studies is that Pto T1 and other crop pathogens may have evolved from ancestors similar to the characterized environmental strains isolated in the French Alps by adapting their effector repertoire to individual crops becoming more virulent on these crops but losing virulence on other plants. / Ph. D.

Pentadesma butyracea Sabine est l’une des quatre espèces du genre Pentadesma endémique de l’Afrique. Elle est distribuée de la Sierra Léone au Gabon dans deux grands types d’habitats :les forêts denses humides discontinues du domaine guinéo-congolais (Haute- et Basse-Guinée) et le domaine soudanien du couloir sec du Dahomey (assimilé à une barrière à l’échange de gènes et d’espèces entre les deux blocs guinéo-congolais). Dans ce dernier, l’espèce se retrouve dans des galeries forestières et occupe une place capitale dans le développement socio-économique des communautés locales en raison des multiples biens et services que procurent ses produits (alimentation, médecine et pharmacopée traditionnelle, etc.). Cependant, des pressions d’origines multiples, telles que le ramassage des graines pour fabriquer du beurre, la fragmentation de l’habitat et sa destruction en faveur du maraîchage, les pratiques culturales inadaptées, les incendies, font peser de lourdes menaces sur l’espèce.<p>Le but de ce travail est d’acquérir les connaissances requises pour la conservation et la gestion durable des ressources génétiques de l’espèce. Trois objectifs ont été définis :(i) étudier la phylogéographie de l’espèce, (ii) étudier sa variabilité morphologique et génétique au Bénin et (iii) caractériser sa biologie de reproduction. En amont de ces travaux, nous avons développé onze marqueurs microsatellites nucléaires chez P. butyracea (chapitre 2). Ils ont été utilisés pour l’étude de la phylogéographie et la diversité génétique de P. butyracea (chapitres 3 et 5), ainsi que pour étudier la dépression de consanguinité et les paramètres de son système de reproduction (chapitre 7).<p>La caractérisation de la répartition spatiale des lignées génétiques de régions intergéniques de l’ADN chloroplastique et de l’ADN ribosomal (ITS) a détecté deux lignées génétiques allopatriques entre le Haut et le Bas-Guinéen, indiquant une forte différenciation génétique et un signal phylogéographique. L’analyse des microsatellites détecte trois pools géniques correspondant aux trois régions étudiées (Haute Guinée, Dahomey Gap et Basse Guinée). La diversité génétique est faible dans le Dahomey Gap, modérée dans le Haut-Guinéen et élevée dans le Bas-Guinéen. Ces résultats indiquent une séparation très ancienne des populations d’Afrique centrale et d’Afrique de l’ouest, alors que celles du Dahomey Gap pourraient résulter des forêts denses humides de l’Afrique de l’ouest lors de la période Holocène humide africaine. Dans ce couloir sec, les populations ont subi une forte dérive génétique, potentiellement due à des évènements de fondation. Au Bénin, deux groupes éco-morphologiques ont été détectés suivant un gradient nord-sud, contrastant avec deux pools géniques présentant une distribution est-ouest. <p>P. butyracea est une espèce auto-compatible majoritairement allogame. La corrélation de paternité est plus élevée aux niveaux intra-fruit vs. inter-fruits, et au sein d’une population de petite taille vs. de grande taille. Les principaux pollinisateurs au Bénin sont deux oiseaux (Cyanomitra verticalis, Cinnyris coccinigastrus) et trois abeilles (Apis mellifera, Meliponula togoensis, Hypotrigona sp.). La productivité totale en fruits augmente en fonction de l’âge de l’arbre et varie en fonction de l’année, atteignant un pic pour les arbres ayant un diamètre de 60-80 cm. Les graines sont récalcitrantes et ont une teneur en eau de 42.5 ± 2.9 %. <p>L’analyse des paramètres de reproduction et de diversité génétique, associés aux facteurs écogéographiques, nous a permis de proposer un échantillon de neuf populations représentatives de la diversité à l’échelle du Bénin, dans la perspective d’une conservation in situ. Le succès de celle-ci dépendra des efforts conjugués des communautés locales, de la recherche forestière et de la définition d’un cadre législatif par le politique pour la protection des habitats. La conservation ex situ est envisagée sous forme d’un verger rassemblant diverses origines, présentant l’intérêt supplémentaire de permettre d’étudier les contributions de la diversité génétique et de la plasticité phénotypique à la variation phénotypique. / Pentadesma butyracea Sabine is one of the four species of the endemic genus Pentadesma in Africa. The species is distributed from Sierra Leone to Gabon in two major types of habitats: the discontinuous and dense Guineo-Congolian rainforests (Upper and Lower Guinea) and the Sudanian domain of the dry corridor of Dahomey (considered as a barrier to the exchange of genes and species between Upper and Lower Guinea). In the latter, the species is found in gallery forests and plays a vital role in the socio-economic livelihood of local communities due to the various resources and services that provide its products (food, medicine and traditional, etc.). However, pressure from many sources including the collection of seeds to make butter, habitat fragmentation and its destruction for market gardening, inadequate agricultural practices, fires, are serious threats to the species.<p>The aim of this work was to acquire appropriate knowledge for the conservation and sustainable management of genetic resources of the species. Three objectives were defined (i) study the phylogeography of the species; (ii) evaluate its morphological and genetic variability in Benin; and (iii) characterize its reproductive biology. In a preliminary work, eleven nuclear microsatellite markers of P. butyracea were developed (Chapter 2). They were used for the study of phylogeography and genetic diversity of P. butyracea (chapters 3 and 5), and to study the inbreeding depression and parameters of its breeding system (Chapter 7).<p>The characterization of the genetic lineages and their spatial distribution using intergenic regions from chloroplast DNA and ribosomal DNA (ITS) region detected two allopatric genetic lineages between Upper and Lower Guinea, indicating a high genetic differentiation and a phylogeographic signal. Microsatellite markers allowed us to detect three genepools matching with the three studied regions (Upper Guinea, Dahomey-Gap and Lower Guinea). Genetic diversity was low in the Dahomey Gap, moderate in Upper Guinea and high in Lower Guinea. These results indicate an ancient separation of populations from Central and West Africa, while those from Dahomey Gap could originate West African rainforests (Upper Guinea) during the African humid Holocene period. In this dry corridor, populations experienced high genetic drift, possibly due to founding events. In Benin, two eco-morphological groups were detected following a north-south gradient, contrasting with two gene pools presenting an east-west distribution.<p>Pentadesma butyracea is a self-compatible, mainly allogamous species. The correlation of paternity was higher within-fruit vs. among-fruits, and in population of small size vs. large size. The main pollinators in Benin are two birds (Cyanomitra verticalis, Cinnyris coccinigastrus) and three bees (Apis mellifera, Meliponula togoensis, Hypotrigona sp.). Total productivity in fruit increases with tree age and varies yearly, reaching a peak for trees of 60-80 cm of diameter class. Seeds are recalcitrant (i.e. they cannot be conserved at low temperature), having a water content of 42.5 ± 2.9% at maturity.<p>The analysis of reproduction and genetics parameters, associated with eco-geographic factors, enabled us to select nine populations representative of the diversity in Benin, from the perspective of in situ conservation. The success of the latter will depend on combined efforts of local communities, forest research and an adequate legislative framework for the protection of habitats. Ex situ conservation is envisaged as an orchard assembling various origins, and would have the additional advantage of allowing to study the contribution of genetic diversity and phenotypic plasticity to phenotypic variation. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

The accurate assessment of forest persistence under environmental change is dependent on the fundamental understanding of the genetic consequences of human intervention and its comparison to that of natural processes, as declines in genetic diversity and changes in its structuring can compromise the adaptive ability of a population. The European beech, Fagus sylvatica, has experienced prolonged human impact over its 14 million ha range with contemporary forests harbouring high ecological, economic, and cultural value. Historical traditional management practices, such as coppicing and pollarding, have impacted a large portion of Europe’s forests. This form of management encouraged vegetative regeneration, prolonging the longevity of individual trees. In several cases, the structure and function of managed trees and their associated ecosystems were significantly altered. Specifically, coppiced beech forests in Europe displayed significantly larger extents of spatial genetic structuring compared to their natural counterparts, revealing a change in the genetic composition of the population due to decades of management. Humans have also aided in the dispersal of beech within and outside of its natural range. In Great Britain, the putative native range retained signals of past colonisation dynamics. However, these signals were obscured by the wide-spread translocation of the species throughout the country. Evidence of post-glacial colonisation dynamics can be found in Sweden as well. In contrast to Britain, the structure of this natural leading range edge displays a gradual reduction in population size where isolation was found to have acted as an effective barrier to gene flow reducing the genetic diversity of populations.

Cette étude vise à comparer l’histoire évolutive des parasitoïdes du genre Horismenus (Hymenoptera: Eulophidae) à celle de leurs hôtes bruches (Coleoptera: Bruchidae) et plante hôte (Phaseolus vulgaris L.) cultivée dans le contexte d’agriculture traditionnelle, au sein de son centre de domestication Mésoaméricain. Nous avons analysé la structure génétique de 23 populations de quatre espèces de parasitoïdes au Mexique, en utilisant un fragment du gène mitochondrial COI afin de les comparer aux structures précédemment publiées des hôtes bruches et du haricot commun. Nous avons prédit que les structures génétiques des populations d’hôtes (bruches et plante) et de parasitoïdes seraient similaires puisque également influencées par la migration entremise par l’humain (HMM) étant donnée que les parasitoïdes se développent telles que les bruches à l’intérieur des haricots. Compte tenu des stratégies de manipulation reproductive utilisées par l’alpha-protéobactérie endosymbionte Wolbachia spp. pour assurer sa transmission, la structure génétique des populations de parasitoïdes inférée à partir du génome mitochondrial devrait être altérée conséquemment à la transmission conjointe des mitochondries et des bactéries lors de la propagation de l’infection dans les populations de parasitoïdes. Les populations du parasitoïde H. missouriensis sont infectées par Wolbachia spp. Tel que prédit, ces populations ne sont pas différenciées (FST = 0,06), ce qui nous empêche d’inférer sur une histoire évolutive parallèle. Contrairement aux bruches, Acanthoscelides obtectus et A. ovelatus, la HMM n'est pas un processus contemporain qui influence la structure génétique des populations du parasitoïde H. depressus, étant donné la forte différenciation (FST = 0,34) qui existe entre ses populations. La structure génétique observée chez H. depressus est similaire à celle de sa plante hôte (i.e. dispersion aléatoire historique à partir d'un pool génique ancestral très diversifié) et est probablement le résultat d’un flux génique important en provenance des populations de parasitoïdes associées aux haricots spontanées à proximité des champs cultivés. L’étude de l’histoire évolutive intégrant plusieurs niveaux trophiques s’est avérée fructueuse dans la détection des différentes réponses évolutives entre les membres du module trophique face aux interactions humaines et parasitaires, et montre la pertinence d’analyser les systèmes écologiques dans leur ensemble. / This study aims to compare the evolutionary history of Horismenus parasitoids (Hymenoptera: Eulophidae) to that of their bruchid beetle hosts (Coleoptera: Bruchidae) and their domesticated host plant (Phaseolus vulgaris L.) in the context of traditional agriculture within their Mesoamerican center of domestication. We analyzed the genetic structure of 23 populations of four Horismenus species in Mexico using COI mitochondrial gene fragments and compared the structures to previously published data on bean plant and beetle hosts. We predicted that because parasitoids complete their development within their beetle hosts, within the bean, the genetic structure of both the host and the parasitoid would be similar and equally influenced by human-mediated migration (HMM). Furthermore, because of reproductive manipulation strategies often used by the alpha-proteobacteria endosymbionte Wolbachia spp. to ensure its transmission, the genetic structure of parasitoid populations inferred from mitochondrial genome would be bias consequently to the conjoint transmission of mitochondria and the bacteria according to propagation of the infection within parasitoids populations. The populations of H. missouriensis parasitoids are infected by Wolbachia spp. As predicted, these populations are not differentiated (FST = 0.06) which prevents us to infer on a parallel evolutionary history. Unlike their bruchids hosts, Acanthoscelides obtectus and A. ovelatus, the HMM is not a contemporary process influencing H. depressus population genetic structure according to the strong populations differentiation (FST = 0.34). The genetic structure observed within H. depressus populations is similar to that of its host plant (i.e. historical random dispersal from a highly diversified ancestral gene pool) and is probably the result of extensive gene flow from parasitoids associated with wild beans populations adjacent to crop fields. The study of evolutionary history integrating multitrophic levels has proved to be fruitful in detecting different evolutionary responses among members of the trophic module face to human and parasite interactions, but also points out the pertinence of analyzing ecological systems as a whole.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Mon étude vise à évaluer la propagation d’une zoonose en émergence au Québec, la maladie de Lyme, en conséquence du réchauffement climatique. Le pathogène responsable de cette infection, Borrelia burgdorferi, est transmis par l’intermédiaire d’une tique parasite, Ixodes scapularis, de plus en plus commune au Québec en raison de l’augmentation de la température moyenne du climat depuis les dernières décennies. Puisque la tique a une capacité de déplacement très restreinte, on s'attend à ce que sa dispersion soit liée à celle de son hôte primaire, soit la souris à pattes blanches (Peromyscus leucopus). Je décrirai donc d’abord les espèces impliquées, leur écologie et leur rôle dans ce système à trois niveaux (hôte/pathogène/vecteur). Puis, à l’aide de séquences d’ADN mitochondrial, je comparerai la phylogéographie des deux principales espèces de souris au Québec, la souris à pattes blanches et la souris sylvestre (P. maniculatus). Des analyses d’arbres et de réseaux d’haplotypes ont révélé des différences significatives dans la structure génétique et ainsi montré que les populations de P. leucopus seraient en expansion dans le sud du Québec. Cette étude nous a finalement permis d’émettre des hypothèses sur le patron d’établissement de la maladie de Lyme au Québec. / My study aims to assess the spread of an emerging zoonosis in Québec, Lyme disease, as a consequence of global warming. The pathogen responsible for this infection, Borrelia burgdorferi, is transmitted through a tick parasite, Ixodes scapularis, increasingly common in Québec due to the elevation of the average temperature of the atmosphere over the past decades. Since the tick has a very limited dispersal capacity, it is expected that its dispersion is linked to that of its primary host, the white-footed mouse (Peromyscus leucopus). I first described the species involved, their ecology and role in this three-level system (host / pathogen / vector). Then, using mitochondrial DNA sequences, I compared the phylogeography of the two main mouse species in Québec, the white-footed mouse and the deer mouse (P. maniculatus). Analyses of trees and haplotype networks revealed significant differences in the genetic structure, and thus showed that populations of P. leucopus are expanding in southern Québec. This study finally allowed making assumptions on the pattern of establishment of Lyme disease in Québec.

En plus des facteurs environnementaux et démographiques, les propriétés génétiques des populations sont devenues une préoccupation majeure pour préserver les populations en déclin de l'extinction. Afin d’acquérir des informations pertinentes pour la planification et la mise en œuvre des stratégies de conservation, les biologistes de la conservation ont réalisé le besoin d’avoir des connaissances en génétique des populations. Grace à l'acquisition de plus en plus rapide et de moins en moins chère d'une large gamme de marqueurs moléculaires, le recours a l’usage de l’outil moléculaire se répand de plus en plus. Ainsi, la génétique de la conservation se confirme comme une discipline à part entière qui est donc l’utilisation de la génétique dans la préservation des espèces comme entités dynamiques capables d'évoluer pour faire face aux changements environnementaux et afin de minimiser leur risque d'extinction. Par le biais de l’utilisation d’un large panel de marqueurs moléculaires (gènes mitochondriaux et nucléaires, microsatellites et SNPs), nous nous sommes intéresse à l’histoire évolutive à différentes échelles spatio-temporelles de la sous-espèce ouest méditerranéenne Testudo. hermanni hermanni (THH), qui présente une distribution insulaire et continentale très fragmentée. Le but de ce travail consiste à 1) comprendre les processus qui expliqueraient la distribution actuelle de la diversité génétique des populations et leur structure, 2) identifier l'origine des populations introduites (à Minorque et au Delta de l’Ebre), et 3) dater l’origine de la sous espèce THH. A l’échelle des populations, il s’agit d’identifier le nombre de groupes génétiques homogènes chez la tortue d’Hermann et le degré de différentiation génétique entre ces groupes afin de définir des unités de conservation évolutivement significatives (ESU) et des unités de gestion (MU). Enfin, nous nous sommes intéresses à l’étude des derniers noyaux de populations de THH dans le Var par des approches de génétique du paysage. Nos résultats ont révélé qu’une divergence par vicariance est à l’ origine de l’apparition de la sous-espèce T.h. hermanni. Ce scenario biogéographique s’expliquerait par les successions d’évènements glaciaires et interglaciaires qu’a connu le Pléistocène depuis plus de 2 MA provoquant un mouvement de retrait de l’espèce vers des zones refuges sur la frange côtière nord-méditerranéenne. Par ailleurs, le patron de différentiation mitochondriale Ile-continent observe et confirme par les microsatellites est très original par rapport à ce qui est connu chez d’autres espèces de reptiles partageant la même aire de distribution. Au vue de l’analyse phylogénétique confirmée par les microsatellites, on peut affirmer que la tortue d’Hermann n’est pas native sur Minorque et qu’elle a une double origine : la première, résultant d’une introduction à partir d’une seule source, probablement d’une population continentale génétiquement proche des Albères. La seconde d'origine insulaire, serait le résultat d’apports multiples, à partir de la Corse, de la Sardaigne ou de la Sicile. Enfin, l’isolement des populations de THH au sein de chaque région géographique reflète une structure génétique très forte. Par conséquent, six unités de gestion (MUs) sont proposées comme unités de conservation et de suivi sur le terrain. / In addition to environmental and demographic factors, the study of genetic properties of populations became inevitable issues in the conservation of declining populations. To acquire relevant information for conservation planning and implementing conservation strategies, conservationists have realized the need of population genetics tools. Moreover, this discipline has become more efficient with the development of a wide range of effective and relatively cheap methods for the characterization of a huge number of molecular markers. This led to define the conservation genetics as a separate discipline, which is the use of genetics in species preservation as dynamic entities evolving to cope with environmental changes and to minimize their extinction risk. Using a broad panel of molecular markers (mitochondrial and nuclear genes, microsatellites and SNPs), we interested in the evolutionary history at different spatial and temporal scales of the Mediterranean western subspecies Testudo hermanni hermanni (THH), which presents a very fragmented insular and continental distribution. The aim of this study is to 1) understand the processes that explain the current distribution of the structure and genetic diversity of populations, 2) identify the origin of introduced populations (Menorca and Ebro Delta) and 3) Dating the origin of the subspecies THH. At the population level, our study aimed to identify the number of homogeneous genetic groups of THH tortoise and the degree of genetic differentiation between these groups in order to identify evolutionarily significant units (ESU) and management units (MU). Finally, we were interested in the study of the last core populations of THH in the Var by landscape genetics approach. Our results revealed that a divergence by vicariance pattern explains the origin of the appearance of the subspecies THH. This biogeographic scenario is explained by the succession of glacial and interglacial events of the Pleistocene causing a withdrawal of the species toward refugia on the northern Mediterranean fringe. Moreover, the observed differentiation pattern (island vs continent) is very original compared to the reported diversity patterns of other reptiles sharing the same distribution range. According to our results, we may conclude that the Hermann’s tortoise is not native in Menorca and has a double origin: the first, is an introduction resulting from a unique source, probably from a continental lineage genetically close to Albera. The second, from an island origin, is the result of multiple contributions, from Corsica, Sardinia or Sicily. Lastly,the isolation of THH populations within each geographic region reflects a very strong genetic structure, therefor the six most relevant management units forconservation purposes are proposed on the basis that they represent a significant part of the evolutionary legacy of the species.

Delimitar espécies e reconstruir a história evolutiva em complexos de espécies pode demandar grandes esforços uma vez que grupos taxonomicamente problemáticos são muitas vezes consequência de eventos de especiação recente ou de rápida especiação. O complexo \'Cattleya coccinea\', da família Orchidaceae, é composto por orquídeas com alto valor ornamental, epifíticas e rupícolas de porte pequeno. Apesar de estarem descritas com caracteres morfológicos diagnósticos claros que permitem sua identificação, a delimitação das espécies atualmente reconhecidas é problemática. Portanto, os objetivos dessa pesquisa foram revisar a delimitação de espécies do complexo e a relação entre as espécies, além de avaliar a diversidade e estrutura genética, aliadas às análises filogeográficas para testar a ocorrência de eventos demográficos históricos. Para responder tais questões foram utilizadas regiões de sequência de cpDNA e nrDNA, 11 locos microssatélites, além de inferência bayesiana e modelo coalescente somadas às estatísticas tradicionais como metodologia. Os resultados suportam o monofiletismo para o clado para as regiões de cpDNA concatenadas. Indicam também quatro grandes eventos de reticulação das espécies do clado C. coccinea com outras espécies do gênero Cattleya. Adicionalmente, suportam o reconhecimento de sete diferentes espécies para o clado C. coccinea, composto por duas principais linhagens evolutivas mais ao norte da região Sudeste: C. brevipedunculata predominante da Serra do Espinhaço e C. wittigiana do norte da Serra do Mar. E cinco espécies distribuídas ao longo da Serra do Mar e Serra da Mantiqueira (C. coccinea, C. mantiqueirae, e mais três espécies correspondentes às populações de DMES; SJPSP e CSRS/JOSC/PMPR. As análises de diversidade mostraram de moderados a altos níveis de diversidade genética e apontam que as espécies C. coccinea e C. brevipedunculata apresentam os maiores níveis de diversidade comparadas a outras espécies do clado. A estruturação genética entre populações dentro de espécies mostrou variação entre níveis baixos a altos. A análise de atribuição de indivíduos a partir de inferência bayesiana mostrou a formação de oito grupos geneticamente distintos. A análise de taxa de dispersão de fluxo gênico pólen x semente mostrou que a dispersão via pólen é aproximadamente oito vezes mais eficiente que a dispersão via sementes somente para C. coccinea. Além disso, a rede de haplótipos indicou que as espécies raramente compartilham haplótipos e que C. coccinea e C. brevipedunculata apresentam maior diversidade com eventos de expansão. A análise de estimativa de tempo de divergência demonstrou que C. brevipedunculata e C. wittigiana provavelmente se originaram entre o Plioceno e o Pleistoceno. As outras espécies do clado se diversificaram no Pleistoceno. Eventos de expansão populacional foram observados para todas as espécies em eras glaciais do Pleistoceno. Por se tratarem de espécies ameaçadas, esse estudo recomenda a conservação \"in situ\" como também a conservação \"ex situ\" de todas as espécies do clado, com atenção especial às duas espécies do Espírito Santo: C. wittigiana e a espécie da localidade DMES, além da espécie da localidade SJPSP em São Paulo. / Species delimitation and reconstruction of the evolutionary history of species complexes may require great efforts since taxonomically problematic groups are often a result of recent speciation events or rapid speciation. The \'Cattleya coccinea\' complex, of the orchid family, consists of epiphytic and small rupicolous orchids with high ornamental value. Despite being described with clear diagnostic morphological characters that allow their identification, delimitation of the currently recognized species is problematic. Therefore, the objectives of this study were to review the species delimitation of the complex and the relationship between species, and to evaluate the genetic diversity and structure, combined with phylogeographic analyzes to test the occurrence of historical demographic events. To answer such questions, cpDNA and nrDNA sequence regions, 11 microsatellite loci, and Bayesian inference and coalescent model were used, combined with traditional statistics and methodology. The results support the monophyly for the clade for concatenated cpDNA regions. They also indicate four major reticulation events of C. coccinea species clade with other species of the genus Cattleya. Additionally, results support the recognition of seven different species for C. coccinea clade, composed of two main evolutionary lineages further north in the Southeast: C. brevipedunculata predominant in the Serra do Espinhaço and C. wittigiana from northern Serra do Mar. And five species distributed along the Serra do Mar and Serra da Mantiqueira (C. coccinea, C. mantiqueirae, and three other species of the populations DMES; SJPSP and CSRS/JOSC/PMPR. The diversity analyzes showed moderate to high levels of genetic diversity and point out that the species C. coccinea and C. brevipedunculata have the highest levels of diversity compared to other species of the clade. The genetic structure of populations within species showed variation from low to high. Assigning individuals analysis from Bayesian inference showed the formation of eight genetically distinct groups. The dispersal rate analysis of pollen x seed gene flow showed that dispersal through pollen is approximately eight times more efficient than the dispersal through seeds only for C. coccinea. Furthermore, the haplotype network indicated that the species rarely share haplotypes and that C.coccinea and C. brevipedunculata present greater diversity with expansion events. The divergence time estimation analysis showed that C. brevipedunculata and C. wittigiana probably originated between the Pliocene and the Pleistocene. The other clade species have diversified in the Pleistocene. Population expansion events were observed for all species in the Pleistocene ice ages. Because they are endangered species, this study recommends the \"in situ\" conservation as well as \"ex situ\" conservation for all species of clade, with special attention for two species of Espírito Santo: C. wittigiana and the species of DMES locality, in addition to the species of SJPSP location in São Paulo.

Els treballs realitzats en aquesta tesi tenen com objectius l'aplicació de la sistemàtica molecular i la filogeografia per resoldre relacions filogenètiques, clarificar la taxonomia i descriure la història de les poblacions de les espècies incloses dins de dos grups de mamífers d'elevat interés conservacionista: els mustélids (família Mustelidae) i els macacs (génere Macaca).L'ús de diferents marcadors genétics mitocondrials (el gen citocrom b i la regió control) i un de nuclear (les seqüencies flanquejants d'una regió repetitiva) ha permés reconstruir les relacions filogenètiques entre 33 espècies de mustelids; delimitar quatre grups filogeogràfics en el teixò euroasiàtic (Meles meles); detectar la venta de productes derivats d'aquesta espècie en països on està protegida; i estudiar el procès d'especiació del macac japonès (Macaca fuscata). A partir dels resultats obtinguts també s'han proposat canvis en la taxonomia d'aquests grups. Al final de la tesi es fan reflexions sobre el paper que desenvolupen els marcadors moleculars en la sistemàtica, sobre com classificar aquelles espècies que no ha finalitzat els seus processos d'especiació i sobre les aplicacions de la sistemàtica, la biologia evolutiva i la genètica en la conservació de la biodiversitat. / The objectives of this thesis were the application of molecular systematics and phylogeography to resolve phylogeny, to clarify taxonomy and to study the population history of species included within two groups of mammals of high conservation interest: the mustelids (Family Mustelidae) and the macaques (Genus Macaca).Using different mitochondrial (cytochrome b gene and control region) and nuclear (flanking sequences of a repetitive region) markers, we have been able to reconstruct the phylogeny of 33 mustelid species; to delimit four phylogeographic groups in the Eurasian badger (Meles meles); to detect the trade of Eurasian badger products in countries where this species is protected; and to study the speciation process of the Japanese macaque (Macaca fuscata). According to our results we have also proposed taxonomic changes in these groups.At the end of the thesis, there are also some reflections about the role of genetic markers in systematics; about how to classify the species that have not finished their speciation process; and about the application of systematics, evolutionary biology and genetics in conservation biology.

Triops cancriformis (Crustacea: Notostraca) occurs in ephemeral habitats like rain pools or floodplain pools distributed over a large geographical range. The named habitats are disturbed by human impacts and, consequently, T. cancriformis is endangered throughout its distribution range. In the present thesis the populated habitats and threats are characterised and further morphological and genetic variations detected among and within European populations are reported. On the basis of recent investigations it is shown that T. cancriformis subspecies separation is hampered by an individual variability which points to the necessity of species revision. The analysis of mitochondrial gene sequence data suggests that the species has colonised most of Europe very recently. The advantage of a complex reproductive strategy in T. cancriformis in this process is discussed. The population structure resolved with nuclear DNA markers highlights that there is low allelic diversity among and within populations compared to other Branchiopoda (Daphnia). By means of the present study it can be shown that habitat conservation is most important to protect T. cancriformis.